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Both Gavin and Susan Drayton, the ship's captain, had worked together to steal the Altair II, though they possessed different intentions at first - Susan's motivation was to combat Japanese whalers, while Gavin aimed to turn it into the mobile Assassin headquarters it now serves as. However, due to Gavin not having the necessary skills to properly captain the ship, Susan was given the position instead.

After the Altair II stopped at Honolulu Harbor on 11 September 2013, Gavin failed to contact the Osaka Assassins. The ship traveled to the Philippines on 1 October 2013, where Emmanuel Barraza, the weapons instructor, re-armed the Altair II crew to prepare for a potential fight in Osaka.

By 1 December 2013, the ship had docked in Osaka, Japan, where it stayed until 1 January 2014, when the Altair II was taken to Tokyo for New Years. During the ship's stay in Japan, its crew were busy discovering and rebuilding the Osaka brotherhood, after which they celebrated the holidays.

By 15 January 2014, the ship had left Japan and was in the Pacific ocean, traveling to the next destination, Russia.

By 19 February 2014, the Altair II had docked in Vladivostok, Russia. After a clue in the book leading to the ship's crew discovering the location of the Russian Assassins, the Altair II sailed around Russia in order to dock in St Petersburg. During this time, Gavin, Emmanuel, and Emmett, having left the ship, went into mainland Russia in order to find the Russian Brotherhood's location.

On March 26th, 2014, the ship docked in St. Petersburg. Gavin, Emmanuel, and Emmett rejoined the crew, along with a new crew member, Galina Voronina.

By 10 May 2014, the Altair II had docked in Helsinki, Finland, where Gavin gave the crew members the order to find William Miles, using clues from the latter's book. Having uncovered the location, the ship then left and by 1 May 2014, the Altair II had arrived at William Miles' bunker in Norway.

Discovering bugs reporting the Assassins' activities to a group called the Initiates, William interrogated a member of Gavin's crew on a daily basis, until all suspects were seen to. Upon gathering their testimonies and reviewing the information over the course of several days, William gathered the crew and subsequently ordered Galina to kill Dr. Stephanie Chiu. Suddenly, Eric Cooper leapt to her defense, explaining he was the spy – however, Stephanie countered this claim by admitting her involvement through uploading his reports. Despite their intervention, William explained the order to simply be a ruse, deciding that the two Initiates were reasonable people and did not deserve execution.